DNA Molecular Weight Calculator
Molecular weight of DNA or RNA from its length or from the exact sequence — dsDNA, ssDNA or RNA, 5′ end chemistry, linear or circular — with mass ↔ pmol ↔ copy-number conversions, molarity from ng/µL, base composition and the A260 extinction coefficient of an oligo.
How it works
From length (NEB): dsDNA MW = bp × 617.96 + 36.04 · ssDNA = nt × 308.97 + 18.02 · RNA = nt × 321.47 + 18.02 g/mol (5′-phosphate ends) · From sequence (OligoCalc): DNA strand = 313.21·A + 289.18·C + 329.21·G + 304.2·T − 61.96 (5′-OH; +79.0 for a 5′-phosphate) · RNA = 329.21·A + 305.18·C + 345.21·G + 306.17·U + 159.0 (5′-triphosphate) · dsDNA = both strands · pmol = ng × 1,000 ÷ MW · copies = mol × 6.022 × 10²³ · nM = (ng/µL) ÷ MW × 10⁶
A nucleic acid’s molecular weight is the sum of its nucleotide residues plus a small correction for what sits on the ends. From a length alone the calculator uses the average residue mass (308.97 g/mol per DNA nucleotide, so 617.96 per base pair, and 321.47 per RNA nucleotide — the values NEB uses) and adds the ends: a 5′-phosphate on a restriction fragment, a 5′-OH on a synthetic oligo or PCR product, a triphosphate on an in vitro transcript, or nothing for a circular plasmid. Paste the sequence instead and every A, C, G and T (or U) is counted with its own mass, the way OligoCalc and oligo suppliers calculate it; for dsDNA the complementary strand is added automatically and IUPAC codes count as the average of the bases they stand for. The molecular weight then converts any mass into moles and copy number (1 µg of a 1 kb dsDNA fragment is about 1.6 pmol, or 9.7 × 10¹¹ copies), a ng/µL reading into nM for ligations and library pooling, and — for single strands — gives the A260 extinction coefficient and what one A260 unit weighs. The older 650 and 660 g/mol per base pair rules of thumb are still available but read about 5% high.
Worked example
A 1,000 bp double-stranded DNA fragment with 5′-phosphates: 1,000 × 617.96 + 36.04 = 617,996 g/mol (618 kDa). One microgram is 1 µg ÷ 617,996 g/mol = 1.618 pmol, or 1.618 × 10⁻¹² × 6.022 × 10²³ = 9.745 × 10¹¹ copies. At 25 ng/µL the fragment is 25 ÷ 617,996 × 10⁶ = 40.5 nM. The M13 forward primer GTAAAACGACGGCCAGT (17 nt, 5′-OH) has 6 A, 4 C, 5 G and 2 T: 6 × 313.21 + 4 × 289.18 + 5 × 329.21 + 2 × 304.2 − 61.96 = 5,228.5 g/mol.
Sources: NEB — NEBioCalculator (dsDNA, ssDNA and RNA mass ↔ moles) · Thermo Fisher — DNA and RNA molecular weights and conversions · OligoCalc — oligonucleotide properties calculator (Kibbe, 2007) · Molecular mass — Wikipedia
Frequently asked questions
Which formula does NEB use?
NEBioCalculator uses 617.96 g/mol per base pair plus 36.04 for dsDNA, 308.97 per nucleotide plus 18.02 for ssDNA and 321.47 plus 18.02 for RNA — the average residue masses with 5′-phosphate ends. That is the default here when you enter a length.
Why does the sequence give a slightly different answer?
GC-rich DNA is heavier than AT-rich DNA (G is 329.21 g/mol, C only 289.18), and the ends depend on how the molecule was made. Counting the actual bases and picking the right ends gives the exact weight; for long fragments the difference from the length-based estimate is usually under 1%.
Why is dsDNA about 618 per base pair but ssDNA about 309?
A base pair is two nucleotides, one on each strand, so its mass is roughly twice that of a single nucleotide. The older 650 and 330 figures are rounded rules of thumb.
How do I get copy number from ng?
Divide the mass by the molecular weight to get moles and multiply by Avogadro’s number (6.022 × 10²³). Enter the amount under More options; the table also lists pmol and copies for 1 pg to 10 µg.
What is a dalton?
A dalton (Da) is the mass unit equal to one gram per mole, so a molecular weight in g/mol is the same number in Da; a kilodalton (kDa) is 1,000 Da.
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Educational estimate, not medical advice — verify formulas, units and assumptions for your specific case.